RetrogeneDB ID: retro_dnov_592

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6603:503480..504035(+)
• Located in intron of: ENSDNOG00000024108

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSDNOG00000000814
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_dnov_592
CCCACCCGCCTGATGAGCTGCAACAGCATCTTGGCCTCAGGACCCCCAGTTTTGGCTTCTACTGCAGCAAGTACAGCCCG
ACAAGGACAGCAGGTGAACCTGGGGCCAGAGCCACAGGTGGGACATGGGATCCATGGTGTTGCCCCTGCAGTGCAGCACC
CCCAGAAAGAGCCATGTCTAACGGAGTTTAAGTACTGCCAAGTGCGGCCAACAGAGGGGGTAAAGTCAGGGGTGTCCAGC
ACACCTCTGACAGACTTCCTGATACAGCTGGAAGATTACACGCCTAAGATCCTAGATGTAGTGACAGTTATTATCTGAAT
CGTGCTGGCTTTGAGGCCTCAGACCCAGGCATAATTTGGCTCATCTCCCTAGATGCTCAGAAATTTATCTCAGATATTGC
CAATGTTGCTTTACAGCACTGCAAAATGAAGGGCACAGCCCCCTGGCAGCTTCCGAAGAAAAAGCAAGGACTGTAAGTAT
ACTTTAAACATGGAAGACCTGACCCCTGCCCTTAAAGAGCATGGCATCAATGTGAAGAAGCCACACTATTCCACC

Alignment

ORF - retro_dnov_592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.49 %
• Parental protein coverage: 84.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PASAAAENKASPAGTAGGAGAGAAAGGTGPVAARAGEPAERRGAAPVSAG-GAAPPEGAMSNGVYVLPSA
          P......N.....G....A...A.....G.......EP....G...V.....AAPPE.AMSNGV.VLPSA
Retrocopy PTRLMSCNSILASGPPVLASTAASTARQGQQVNLGPEPQVGHGIHGVAPA<SAAPPERAMSNGV*VLPSA

Parental  ANGE-VKPVVSSTPLVDFLMQLEDYTPTIPDAVT-GYYLNRAGFEASDPRIIRLISLAAQKFISDIANDA
          AN...VK..VSSTPL.DFL.QLEDYTP.I.D.VT..YYLNRAGFEASDP.II.LISL.AQKFISDIAN.A
Retrocopy ANRG>VKSGVSSTPLTDFLIQLEDYTPKILDVVT<SYYLNRAGFEASDPGIIWLISLDAQKFISDIANVA

Parental  LQHCKMKGTA-SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYFT
          LQHCKMKGTA..GS.R.KSKD.KYTL.MEDLTPAL.E.GINVKKPHY.T
Retrocopy LQHCKMKGTA>PGSFRRKSKDCKYTLNMEDLTPALKEHGINVKKPHYST

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	79.34 RPM
SRP012922_cerebellum	0.00 RPM	44.40 RPM
SRP012922_heart	0.00 RPM	38.75 RPM
SRP012922_kidney	0.00 RPM	122.39 RPM
SRP012922_liver	0.00 RPM	46.75 RPM
SRP012922_lung	0.00 RPM	72.39 RPM
SRP012922_quadricep_muscle	0.00 RPM	37.56 RPM
SRP012922_spleen	0.00 RPM	74.06 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_592 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016278	2 retrocopies	retro_amel_1088, retro_amel_297,
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592 ,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542, retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Loxodonta africana	ENSLAFG00000029330	1 retrocopy	retro_lafr_750,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,